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Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.

Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, Fontanesi L - PLoS ONE (2015)

Bottom Line: Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca).Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads.The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy; Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy.

ABSTRACT
Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

No MeSH data available.


Densities of donkey single nucleotide polymorphisms: Box plot of the distribution by chromosomes of the SNP density in 1-Mb windows.Quartiles are the edges of the box. The edges of the boxes correspond to quartiles; the notches are the standard errors of the median; and the vertical bars to the range.
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pone.0131925.g007: Densities of donkey single nucleotide polymorphisms: Box plot of the distribution by chromosomes of the SNP density in 1-Mb windows.Quartiles are the edges of the box. The edges of the boxes correspond to quartiles; the notches are the standard errors of the median; and the vertical bars to the range.

Mentions: The total number of SNPs divided by horse chromosomes and their densities are reported in Figs 5, 6 and 7, respectively. A comparison between autosomal and X chromosome SNPs detected in the donkey genome with differences between the horse and donkey genome, projected on the horse chromosomes can be obtained from Fig 7 and S1 Fig. It is interesting to note that for the corresponding donkey reads mapping on horse chromosome 12 (ECA12), a higher density of SNPs was observed in all three donkeys and two sequencing platforms, reducing the possibilities of a systematic error. The reason for this higher SNP density is not known. However, it is interesting to note that four independent studies [63–66] reported that ECA12 was the most enriched horse chromosome of copy number variations (CNVs). Copy number variation might contribute to increase the level of variability in different allelic copies that can subsequently evolve in the constitution of gene duplications [67]. The ECA12 is homologous with the donkey chromosome 17 (EAS17), as demonstrated by comparative FISH mapping and chromosome specific painting experiments between these two species [30–32]. Considering that in close species conserved structural duplications could produce recurrent interspecies CNV [68, 69], a high density of CNV might be also present in EAS17, producing also a higher density of single nucleotide variants that cannot be distinguished from true allelic SNPs using only sequencing reads. Distribution of different SNP densities across chromosomes and chromosome regions are evident from Figs 6 and 7. The level of SNP density seems to follow in parallel the nucleotide divergence ratio between horse and donkeys. In particular a lower SNP density can be observed on chromosome X, as expected according to previous studies in other mammals [54, 56, 70].


Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.

Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, Fontanesi L - PLoS ONE (2015)

Densities of donkey single nucleotide polymorphisms: Box plot of the distribution by chromosomes of the SNP density in 1-Mb windows.Quartiles are the edges of the box. The edges of the boxes correspond to quartiles; the notches are the standard errors of the median; and the vertical bars to the range.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4495037&req=5

pone.0131925.g007: Densities of donkey single nucleotide polymorphisms: Box plot of the distribution by chromosomes of the SNP density in 1-Mb windows.Quartiles are the edges of the box. The edges of the boxes correspond to quartiles; the notches are the standard errors of the median; and the vertical bars to the range.
Mentions: The total number of SNPs divided by horse chromosomes and their densities are reported in Figs 5, 6 and 7, respectively. A comparison between autosomal and X chromosome SNPs detected in the donkey genome with differences between the horse and donkey genome, projected on the horse chromosomes can be obtained from Fig 7 and S1 Fig. It is interesting to note that for the corresponding donkey reads mapping on horse chromosome 12 (ECA12), a higher density of SNPs was observed in all three donkeys and two sequencing platforms, reducing the possibilities of a systematic error. The reason for this higher SNP density is not known. However, it is interesting to note that four independent studies [63–66] reported that ECA12 was the most enriched horse chromosome of copy number variations (CNVs). Copy number variation might contribute to increase the level of variability in different allelic copies that can subsequently evolve in the constitution of gene duplications [67]. The ECA12 is homologous with the donkey chromosome 17 (EAS17), as demonstrated by comparative FISH mapping and chromosome specific painting experiments between these two species [30–32]. Considering that in close species conserved structural duplications could produce recurrent interspecies CNV [68, 69], a high density of CNV might be also present in EAS17, producing also a higher density of single nucleotide variants that cannot be distinguished from true allelic SNPs using only sequencing reads. Distribution of different SNP densities across chromosomes and chromosome regions are evident from Figs 6 and 7. The level of SNP density seems to follow in parallel the nucleotide divergence ratio between horse and donkeys. In particular a lower SNP density can be observed on chromosome X, as expected according to previous studies in other mammals [54, 56, 70].

Bottom Line: Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca).Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads.The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy; Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy.

ABSTRACT
Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

No MeSH data available.